Data and Computational Biology Group UNIMIB (was BI*oinformatics MI*lan B*icocca)
The github organization of the DCB group of the DISCo, Università degli Studi di Milano Bicocca
Pinned Repositories
J-Space.jl
J-SPACE is a Julia package to simulate the spatial growth and the genomic evolution of a cell population and the experiment of sequencing the genome of the sampled cells.
LACE
LACE 2.0 is a new release of the LACE R Bioconductor package, which provides an interactive user interface to perform clonal evolution analyses for single-cell sequencing data, including longitudinal experiments. The tool also allows to annotate and retrieve the relevant variants based on user-defined criteria.
oral_squamous_longitudinal
Utilities repository to analyze single-cell data from https://www.nature.com/articles/s41467-018-07261-3.
PiCnIc-COADREAD
PiCnIc implementation for COADREAD
PMCE
GitHub repository of the PMCE Framework. F. Angaroni, K. Chen, C. Damiani, G. Caravagna, A. Graudenzi, D. Ramazotti, PMCE: efficient inference of expressive models of cancer evolution with high prognostic power, Bioinformatics, 2021; btab717, https://doi.org/10.1093/bioinformatics/btab717
review-scRNA-seq-DENOISING
scFBA
TRaIT
Source code and input data to reproduce the case studies presented in the TRaIT framework: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-019-2795-4
TRONCO
Repository of the TRanslational ONCOlogy library, which includes various algorithms (such as CAPRESE and CAPRI) and the Pipeline for Cancer Inference (PICNIC).
VERSO
Viral Evolution ReconStructiOn (VERSO). The manuscript of the method is available at: https://www.cell.com/patterns/fulltext/S2666-3899(21)00022-2
Data and Computational Biology Group UNIMIB (was BI*oinformatics MI*lan B*icocca)'s Repositories
BIMIB-DISCo/oral_squamous_longitudinal
Utilities repository to analyze single-cell data from https://www.nature.com/articles/s41467-018-07261-3.
BIMIB-DISCo/PiCnIc-COADREAD
PiCnIc implementation for COADREAD
BIMIB-DISCo/MaREA
Metabolic feature extraction, enrichment and visualization of transcriptomic data
BIMIB-DISCo/MST
MST testing
BIMIB-DISCo/popFBA
popFBA COBRA Toolbox function
BIMIB-DISCo/cyTRON
cyTRON: a Cytoscape app for the visualization of evolutionary trajectories in cancer progression. The app is also available at the Cytoscape App Store at http://apps.cytoscape.org/apps/cytron
BIMIB-DISCo/CABERNET
CABerNET: CABeRNET: a Cytoscape app for Augmented Boolean models of gene Regulatory NETworks
BIMIB-DISCo/datasets
BIMIB-DISCo/MALDI-PxP
The code relative to the MALDI PxP project for the analysis of proteomic data.
BIMIB-DISCo/mutex
Automatically exported from code.google.com/p/mutex
BIMIB-DISCo/Neuromorph-Calibration-Paper
Automatic calibration of neuromorphic chips